Merge pull request #1340 from sagely1/AG-1565-remove-druggability

AG-1565 remove druggability
Sage-Bionetworks · Dec 16, 2024 · 4524665 · 4524665
2 parents 40b2ca1 + 57fa18a
commit 4524665
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Showing 7 changed files with 3 additions and 130 deletions.
diff --git a/package.json b/package.json
@@ -1,8 +1,8 @@
 {
   "name": "agora",
-  "version": "3.4.0",
+  "version": "3.5.0",
   "data-file": "syn13363290",
-  "data-version": "70",
+  "data-version": "71",
   "private": true,
   "scripts": {
     "dev": "concurrently --kill-others \"npm:dev:server\" \"npm:dev:app\"",

diff --git a/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts b/src/app/features/genes/components/gene-nominated-targets/gene-nominated-targets.component.ts
@@ -56,21 +56,6 @@ export class GeneNominatedTargetsComponent implements OnInit {
       header: 'Pharos Class',
       selected: false,
     },
-    {
-      field: 'sm_druggability_display_value',
-      header: 'Small Molecule Druggability',
-      selected: false,
-    },
-    {
-      field: 'safety_rating_display_value',
-      header: 'Safety Rating',
-      selected: false,
-    },
-    {
-      field: 'ab_modality_display_value',
-      header: 'Antibody Modality',
-      selected: false,
-    },
   ];
 
   constructor(private apiService: ApiService) {}
@@ -138,23 +123,8 @@ export class GeneNominatedTargetsComponent implements OnInit {
           de.pharos_class_display_value = de.druggability[0].pharos_class
             ? de.druggability[0].pharos_class
             : 'No value';
-          de.sm_druggability_display_value =
-            de.druggability[0].sm_druggability_bucket +
-            ': ' +
-            de.druggability[0].classification;
-          de.safety_rating_display_value =
-            de.druggability[0].safety_bucket +
-            ': ' +
-            de.druggability[0].safety_bucket_definition;
-          de.ab_modality_display_value =
-            de.druggability[0].abability_bucket +
-            ': ' +
-            de.druggability[0].abability_bucket_definition;
         } else {
           de.pharos_class_display_value = 'No value';
-          de.sm_druggability_display_value = 'No value';
-          de.safety_rating_display_value = 'No value';
-          de.ab_modality_display_value = 'No value';
         }
       });
 

diff --git a/src/app/features/genes/components/gene-similar/gene-similar.component.ts b/src/app/features/genes/components/gene-similar/gene-similar.component.ts
@@ -45,12 +45,6 @@ export class GeneSimilarComponent implements OnInit {
       header: 'Protein Expression Change',
     },
     { field: 'pharos_class_display_value', header: 'Pharos Class' },
-    {
-      field: 'sm_druggability_display_value',
-      header: 'Small Molecule Druggability',
-    },
-    { field: 'safety_rating_display_value', header: 'Safety Rating' },
-    { field: 'ab_modality_display_value', header: 'Antibody Modality' },
   ];
 
   gctLink: { [key: string]: string } | undefined;
@@ -117,23 +111,8 @@ export class GeneSimilarComponent implements OnInit {
           de.pharos_class_display_value = de.druggability[0].pharos_class
             ? de.druggability[0].pharos_class
             : 'No value';
-          de.sm_druggability_display_value =
-            de.druggability[0].sm_druggability_bucket +
-            ': ' +
-            de.druggability[0].classification;
-          de.safety_rating_display_value =
-            de.druggability[0].safety_bucket +
-            ': ' +
-            de.druggability[0].safety_bucket_definition;
-          de.ab_modality_display_value =
-            de.druggability[0].abability_bucket +
-            ': ' +
-            de.druggability[0].abability_bucket_definition;
         } else {
           de.pharos_class_display_value = 'No value';
-          de.sm_druggability_display_value = 'No value';
-          de.safety_rating_display_value = 'No value';
-          de.ab_modality_display_value = 'No value';
         }
       });
 

diff --git a/src/app/features/genes/components/gene-table/gene-table.component.ts b/src/app/features/genes/components/gene-table/gene-table.component.ts
@@ -116,20 +116,7 @@ export class GeneTableComponent implements OnInit {
       } else if (a == null && b == null) {
         result = 0;
       } else if (typeof a === 'string' && typeof b === 'string') {
-        // Natural sorting for this score type, which can be >= 10
-        if (event.field === 'sm_druggability_display_value'
-          || event.field === 'safety_rating_display_value'
-          || event.field === 'ab_modality_display_value') {
-          let nA = parseInt(a.split(':')[0], 10);
-          let nB = parseInt(b.split(':')[0], 10);
-
-          nA = !isNaN(nA) ? nA : 999 * event.order;
-          nB = !isNaN(nB) ? nB : 999 * event.order;
-
-          result = nA < nB ? -1 : nA > nB ? 1 : 0;
-        } else {
-          result = a.localeCompare(b);
-        }
+        result = a.localeCompare(b);
       } else {
         result = a < b ? -1 : a > b ? 1 : 0;
       }

diff --git a/src/app/models/genes.ts b/src/app/models/genes.ts
@@ -85,9 +85,6 @@ export interface Gene {
   similar_genes_network?: SimilarGenesNetwork;
 
   // Similar table (not in mongo document)
-  ab_modality_display_value?: string;
-  safety_rating_display_value?: string;
-  sm_druggability_display_value?: string;
   pharos_class_display_value?: string;
   is_any_rna_changed_in_ad_brain_display_value?: string;
   is_any_protein_changed_in_ad_brain_display_value?: string;

diff --git a/tests/nominated-targets.spec.ts b/tests/nominated-targets.spec.ts
@@ -9,57 +9,4 @@ test.describe('specific viewport block', () => {
     // Expect a title "to contain" a substring.
     await expect(page).toHaveTitle('Nominated Targets | Candidate genes for AD treatment or prevention');
   });
-
-  test('has correct sort on druggability columns', async ({ page }) => {
-    await page.goto('/genes/nominated-targets');
-
-    await expect(page.locator('table')).toBeVisible();
-
-    await page.locator('#pr_id_3 span').click();
-
-    await page.getByLabel('Nominations').click();
-    await page.getByLabel('Year First Nominated').click();
-    await page.getByLabel('Nominating Teams').click();
-    await page.getByLabel('Cohort Study').click();
-    await page.getByLabel('Small Molecule Druggability').click();
-    await page.getByLabel('Safety Rating').click();
-    await page.getByLabel('Antibody Modality').click();
-
-    // sort forward on small molecule druggability
-    await page.getByRole('cell', { name: 'Small Molecule Druggability' }).click();
-
-    const row = page.locator('table tr:nth-child(2)');
-    let cell = row.getByRole('cell').nth(1);
-    await expect(cell).not.toContainText('No Value');
-
-    // sort reverse on small molecule druggability
-    await page.getByRole('cell', { name: 'Small Molecule Druggability' }).click();
-
-    cell = row.getByRole('cell').nth(1); 
-    await expect(cell).not.toContainText('No Value');
-
-    // sort forward on safety rating
-    await page.getByRole('cell', { name: 'Safety Rating' }).click();
-
-    cell = row.getByRole('cell').nth(2);
-    await expect(cell).not.toContainText('No Value');
-
-    // sort reverse on safety rating
-    await page.getByRole('cell', { name: 'Safety Rating' }).click();
-
-    cell = row.getByRole('cell').nth(2); 
-    await expect(cell).not.toContainText('No Value');
-
-    // sort forward on antibody modality
-    await page.getByRole('cell', { name: 'Antibody Modality' }).click();
-
-    cell = row.getByRole('cell').nth(3);
-    await expect(cell).not.toContainText('No Value');
-
-    // sort reverse on antibody modality
-    await page.getByRole('cell', { name: 'Antibody Modality' }).click();
-
-    cell = row.getByRole('cell').nth(3); 
-    await expect(cell).not.toContainText('No Value');
-  });
 });
diff --git a/tests/similar-genes.spec.ts b/tests/similar-genes.spec.ts
@@ -20,12 +20,5 @@ test.describe('specific viewport block', () => {
 
     const cell = await page.getByRole('row').nth(1).getByRole('cell').nth(1).innerText();
     expect(cell).not.toBe('');
-
-
-    // sort reverse on small molecule druggability
-    await page.getByRole('cell', { name: 'Nominated Target' }).click();
-
-    const cell2 = await page.getByRole('row').nth(1).getByRole('cell').nth(1).innerText();
-    expect(cell2).not.toBe('');
   });
 });